Sequence Alignments with BioEdit
BioEdit is designed for the scientists and laboratory technicians that work with biological sequences. It is basically a text editor enhanced with features specific to sequence alignment. Downloading sequences from genbank & manipulating them in bioedit The Bio-Web: Resources for Molecular and Cell Biologists is a non-commercial, educational site with the only purpose of facilitating access to biology-related information over the internet. First, BioEdit is a program available on Windows platform only. If you want to run it on your Mac, you will need to install a desktop virtualization software such as VMware fusion. 2017-2-22 Bioedit(分子生物学应用软件) 等级: 免费版 2017-02-22 11:56:34 12 MB 简体中文 下载推荐理由:这是Bioedit(分子生物学应用软件),是一个功能齐全的免费分子生物学应用软件,可以完成核苷酸序列和蛋白质序列进行所有常规的分析操作,如:序列比对、序列检索、引物设计、系统发育分析等。. Dsi action replay driver for mac.
BioEdit is, among other things, an alignment editor, although it has many more capabilities. It is available free from the Department of Molecular Biology at North Carolina State University.It will work with sequence alignments in many forms, including GenBank and the cross-platform FASTA (FAST Alignment) format. In this example, we will use the FASTA format. Here is an example of that format:
>gi|112927|sp|P05067|A4_HUMAN Amyloid beta A4 protein precursor (APP) (ABPP)
MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGIL
QYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQER
MDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWW
MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGIL
QYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKFLHQER
MDVCETHLHWHTVAKETCSEKSTNLHDYGMLLPCGIDKFRGVEFVCCPLAEESDNVDSADAEEDDSDVWW
The above is a portion of the sequence of a protein. The first line must always begin with > and is a comment or identification line. This is followed by the sequence, using the one letter codes for bases or amino acids. The length of the lines is irrelevant.
BioEdit by itself is capable of pairwise alignment only. However, the program ClustalW come with it, is installed in a subdirectory, and can be run from within BioEdit to create multiple alignments. Consult the Help file to learn how to configure this option.
To do a pairwise alignment:
- Use File/Open to read in the first sequence, choosing the appropriate file format
- Read in the second with File/Import
- Both sequences will now appear in the main window
- If you are aligning nucleic acid sequence, the program will automatically chose an Identity matrix for scoring; for proteins, you must choose your scoring matrix (explained below) using Sequence/Similarity Matrix. Blosum62 is the default.
- Hold down the Control key and click on the titles of both sequences to select them
- Now select Sequence/Pairwise Alignment. You will be offered two options
- Optimal global alignment; this will maximize the number of matches, allowing gaps
- Allow ends to slide keeps the sequences intact and slides one sequence as a whole relative to the other
- Make your choice; a window will pop up with the score for your alignment and the aligned sequences will appear in the main window:
To make a nicely colored version of the alignment, select File/Graphic View 3d max 11 mac torrent.
- You can now fill in background colors for identical and similar residues
- Click on the boxes labeled 'Similar' and 'Identical' to choose background and foreground colors
- Check Identity/similarity shading (lower left) to have your choices take effect
- Other formatting choices:
- Position the titles left or right or truncate them using the appropriate check boxes
- Use the check box to group the residues in blocks of ten, and the scroll box to limit the width of the display to your window
- Choose File/Copy as Bitmap or File/Copy as Enhanced Windows Metafile to copy your prettied up alignment to the clipboard. From there, you can paste it into Word or your favorite graphic program.
Here's what the Graphic View window will look like when you're done: Advanced file renamer.
BioEdit will also translate DNA or RNA to protein, find cDNA or the reverse complement, do a nice analysis with bar graph of the percentages of the four bases, and otherwise characterize your sequence.
For example, with your human elastase gene loaded and selected, choose Sequence/Nucleic Acid/Translate/Frame 1. You will get a new window containing the translation. Try this when you have a sequence displayed in Graphic View also.
Similarity Matrices Any alignment requires some method of judging the quality of fit between the two or more sequences. Any scoring scheme must account for gaps (which we saw in our alignment of the two elastase genes), substitutions, and insertions and deletions.
For nucleic acids, the scoring scheme can be relatively simple; since only for characters occur in the sequences, substitutions are generally not present. BioEdit uses the following values:
Variation | Score |
---|---|
Match | 2 |
Mismatch | -1 |
Gap Initiation | -3 |
Extending Gap by 1 | -1 |
Such a scoring system allows us to compare several possible alignment and choose the 'best' - the one with the highest score.
![Bioedit 7.2.6.1 Bioedit 7.2.6.1](https://jorgensen.biology.utah.edu/wayned/ape/Images/text_map.gif)
Bioedit Alignment
In proteins, amino acid substitutions occur frequently, especially among amino acid of similar physicochemical properties. Alanine (methyl side chain) and valine (isopropyl side chain) are common substitutions for each other, that can occur without making a significant difference in the properties of a protein. Hence, more complicated schemes than that above are required to score alignments.
Perhaps the most widely used scoring matrices for proteins are the BLOSUM (blocks substitution matrix) developed by S. and J. G. Henikoff ['Amino acid substitution matrices from protein blocks', Proc. Natl. Acad. Sci. 1992, 89 10915-10919.].
- From regions of closely related proteins that can be aligned without gaps, they calculated the ratio of observed pairs at any position to the number expected from overal amino acid frequencies
- The results are expressed as the log of this ratio, multiplied by 10 to avoid decimals
- Depending on the particular sequences used, several matrices have been developed; BLOSUM62 is the most common.
![Bioedit Bioedit](https://img.informer.com/screenshots/3679/3679082_1_4.png)
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A | R | N | D | C | Q | E | G | H | I | L | K | M | F | P | S | T | W | Y | V | B | Z | X | * | |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A | 4 | -1 | -2 | -2 | 0 | -1 | -1 | 0 | -2 | -1 | -1 | -1 | -1 | -2 | -1 | 1 | 0 | -3 | -2 | 0 | -2 | -1 | 0 | -4 |
R | -1 | 5 | 0 | -2 | -3 | 1 | 0 | -2 | 0 | -3 | -2 | 2 | -1 | -3 | -2 | -1 | -1 | -3 | -2 | -3 | -1 | 0 | -1 | -4 |
N | -2 | 0 | 6 | 1 | -3 | 0 | 0 | 0 | 1 | -3 | -3 | 0 | -2 | -3 | -2 | 1 | 0 | -4 | -2 | -3 | 3 | 0 | -1 | -4 |
D | -2 | -2 | 1 | 6 | -3 | 0 | 2 | -1 | -1 | -3 | -4 | -1 | -3 | -3 | -1 | 0 | -1 | -4 | -3 | -3 | 4 | 1 | -1 | -4 |
C | 0 | -3 | -3 | -3 | 9 | -3 | -4 | -3 | -3 | -1 | -1 | -3 | -1 | -2 | -3 | -1 | -1 | -2 | -2 | -1 | -3 | -3 | -2 | -4 |
Q | -1 | 1 | 0 | 0 | -3 | 5 | 2 | -2 | 0 | -3 | -2 | 1 | 0 | -3 | -1 | 0 | -1 | -2 | -1 | -2 | 0 | 3 | -1 | -4 |
E | -1 | 0 | 0 | 2 | -4 | 2 | 5 | -2 | 0 | -3 | -3 | 1 | -2 | -3 | -1 | 0 | -1 | -3 | -2 | -2 | 1 | 4 | -1 | -4 |
G | 0 | -2 | 0 | -1 | -3 | -2 | -2 | 6 | -2 | -4 | -4 | -2 | -3 | -3 | -2 | 0 | -2 | -2 | -3 | -3 | -1 | -2 | -1 | -4 |
H | -2 | 0 | 1 | -1 | -3 | 0 | 0 | -2 | 8 | -3 | -3 | -1 | -2 | -1 | -2 | -1 | -2 | -2 | 2 | -3 | 0 | 0 | -1 | -4 |
I | -1 | -3 | -3 | -3 | -1 | -3 | -3 | -4 | -3 | 4 | 2 | -3 | 1 | 0 | -3 | -2 | -1 | -3 | -1 | 3 | -3 | -3 | -1 | -4 |
L | -1 | -2 | -3 | -4 | -1 | -2 | -3 | -4 | -3 | 2 | 4 | -2 | 2 | 0 | -3 | -2 | -1 | -2 | -1 | 1 | -4 | -3 | -1 | -4 |
K | -1 | 2 | 0 | -1 | -3 | 1 | 1 | -2 | -1 | -3 | -2 | 5 | -1 | -3 | -1 | 0 | -1 | -3 | -2 | -2 | 0 | 1 | -1 | -4 |
M | -1 | -1 | -2 | -3 | -1 | 0 | -2 | -3 | -2 | 1 | 2 | -1 | 5 | 0 | -2 | -1 | -1 | -1 | -1 | 1 | -3 | -1 | -1 | -4 |
F | -2 | -3 | -3 | -3 | -2 | -3 | -3 | -3 | -1 | 0 | 0 | -3 | 0 | 6 | -4 | -2 | -2 | 1 | 3 | -1 | -3 | -3 | -1 | -4 |
P | -1 | -2 | -2 | -1 | -3 | -1 | -1 | -2 | -2 | -3 | -3 | -1 | -2 | -4 | 7 | -1 | -1 | -4 | -3 | -2 | -2 | -1 | -2 | -4 |
S | 1 | -1 | 1 | 0 | -1 | 0 | 0 | 0 | -1 | -2 | -2 | 0 | -1 | -2 | -1 | 4 | 1 | -3 | -2 | -2 | 0 | 0 | 0 | -4 |
T | 0 | -1 | 0 | -1 | -1 | -1 | -1 | -2 | -2 | -1 | -1 | -1 | -1 | -2 | -1 | 1 | 5 | -2 | -2 | 0 | -1 | -1 | 0 | -4 |
W | -3 | -3 | -4 | -4 | -2 | -2 | -3 | -2 | -2 | -3 | -2 | -3 | -1 | 1 | -4 | -3 | -2 | 11 | 2 | -3 | -4 | -3 | -2 | -4 |
Y | -2 | -2 | -2 | -3 | -2 | -1 | -2 | -3 | 2 | -1 | -1 | -2 | -1 | 3 | -3 | -2 | -2 | 2 | 7 | -1 | -3 | -2 | -1 | -4 |
V | 0 | -3 | -3 | -3 | -1 | -2 | -2 | -3 | -3 | 3 | 1 | -2 | 1 | -1 | -2 | -2 | 0 | -3 | -1 | 4 | -3 | -2 | -1 | -4 |
B | -2 | -1 | 3 | 4 | -3 | 0 | 1 | -1 | 0 | -3 | -4 | 0 | -3 | -3 | -2 | 0 | -1 | -4 | -3 | -3 | 4 | 1 | -1 | -4 |
Z | -1 | 0 | 0 | 1 | -3 | 3 | 4 | -2 | 0 | -3 | -3 | 1 | -1 | -3 | -1 | 0 | -1 | -3 | -2 | -2 | 1 | 4 | -1 | -4 |
X | 0 | -1 | -1 | -1 | -2 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -1 | -2 | 0 | 0 | -2 | -1 | -1 | -1 | -1 | -1 | -4 |
* | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | -4 | 1 |
To look up the value corresponding to the substitution 'N->W' (an Asparagine is replaced by a Tryptophan), go to the line of the table labeled 'N' and follow this line until you get to the column labeled 'W': -4. The substitution 'N->W' is not very likely; that is, it does not occur often in closely related proteins. On the other hand, the substitution 'V->I' (BLOSUM score: 3) is very likely.
BioEdit itself can only do pairwise alignments. However, the download includes a copy of the multiple alignment tool ClustalW, which can align many sequences. You can use this directly, or configure BioEdit to run it for you.
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